Mercurial > repos > ppericard > mixomics_blocksplsda
comparison matCor_addVar_wrapper.R @ 3:0a3c83f2197a draft
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
author | ppericard |
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date | Fri, 25 Oct 2019 07:10:59 -0400 |
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2:655d1fbcd3e6 | 3:0a3c83f2197a |
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1 #!/usr/bin/env Rscript | |
2 | |
3 # Setup R error handling to go to stderr | |
4 options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) | |
5 | |
6 # we need that to not crash galaxy with an UTF8 error on German LC settings. | |
7 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") | |
8 | |
9 ## Get parameters ## | |
10 suppressPackageStartupMessages(require(argparse)) | |
11 | |
12 parser <- ArgumentParser(description='Compute the matCorEtBlockSelect and addVariablesReponses functions') | |
13 | |
14 parser$add_argument('--input_rdata', dest='input_rdata', required=TRUE, help="Input RData file") | |
15 parser$add_argument('--cutoff_comp', dest='cutoff_comp', type='double', required=TRUE, help="") | |
16 parser$add_argument('--mat_block_Y_file', dest='mat_block_Y_file', required=TRUE, help="Matrix block Y filepath") | |
17 parser$add_argument('--output_rdata', dest='output_rdata', required=TRUE, help="Output RData file") | |
18 parser$add_argument('--output_blocks_comb', dest='output_blocks_comb', required=TRUE, help="Output blocks combinations file") | |
19 | |
20 args <- parser$parse_args() | |
21 | |
22 ## Print parameters | |
23 print("Input RData:") | |
24 print(args$input_rdata) | |
25 print("Cutoff comp:") | |
26 print(args$cutoff_comp) | |
27 print("Mat Block Y file:") | |
28 print(args$mat_block_Y_file) | |
29 print("Output RData:") | |
30 print(args$output_rdata) | |
31 print("Output Blocks combinations:") | |
32 print(args$output_blocks_comb) | |
33 | |
34 ## Loading libraries | |
35 suppressPackageStartupMessages(require(mixOmics)) | |
36 | |
37 # R script call | |
38 source_local <- function(fname) | |
39 { | |
40 argv <- commandArgs(trailingOnly = FALSE) | |
41 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)) | |
42 source(paste(base_dir, fname, sep="/")) | |
43 } | |
44 ## Loading local functions | |
45 source_local("Integration_block_splsda_fonc.R") | |
46 | |
47 load(args$input_rdata) | |
48 | |
49 liste_matCorEtBlockSelect = matCorEtBlockSelect(res_block_splsda = mixomics_result, | |
50 cutoff_comp = args$cutoff_comp, | |
51 comp = 1:2) | |
52 | |
53 mat_cor_comp1 = liste_matCorEtBlockSelect$mat_cor_comp1 | |
54 mat_cor_comp2 = liste_matCorEtBlockSelect$mat_cor_comp2 | |
55 dataframe_cor_comp_var_global = liste_matCorEtBlockSelect$dataframe_cor_comp_var_global | |
56 liste_vec_indice_blockSelect = liste_matCorEtBlockSelect$liste_vec_indice_blockSelect | |
57 liste_vec_blocks = liste_matCorEtBlockSelect$liste_vec_blocks | |
58 | |
59 print("Mat cor comp1:") | |
60 print(mat_cor_comp1) | |
61 print("Mat cor comp2:") | |
62 print(mat_cor_comp2) | |
63 print("dataframe_cor_comp_var_global:") | |
64 print(dataframe_cor_comp_var_global) | |
65 print("liste_vec_indice_blockSelect:") | |
66 print(liste_vec_indice_blockSelect) | |
67 print("liste_vec_blocks:") | |
68 print(liste_vec_blocks) | |
69 | |
70 | |
71 lapply(liste_vec_blocks, write, file=args$output_blocks_comb, append=TRUE, ncolumns=100, sep=",") | |
72 | |
73 | |
74 print("Reading Mat Block Y") | |
75 mat_block_Y = read.table(args$mat_block_Y_file, header=TRUE, row.names=1) | |
76 print(mat_block_Y) | |
77 | |
78 | |
79 liste_dataframe_cor_comp_var_global = addVariablesReponses(res_block_splsda = mixomics_result, | |
80 dataframe_cor_comp_var_global = dataframe_cor_comp_var_global, | |
81 liste_vec_indice_blockSelect = liste_vec_indice_blockSelect, | |
82 mat_block_Y = mat_block_Y) | |
83 | |
84 | |
85 save(mixomics_result, | |
86 liste_matCorEtBlockSelect, | |
87 mat_cor_comp1, | |
88 mat_cor_comp2, | |
89 dataframe_cor_comp_var_global, | |
90 liste_vec_indice_blockSelect, | |
91 liste_vec_blocks, | |
92 liste_dataframe_cor_comp_var_global, | |
93 file = args$output_rdata) |